A Spell I Can't Undo
by Coqui's Song
Summary: The war against demons is won, but Valentine still searches for the Mortal Cup. Jocelyn drops Clary off to be raised by Magnus, fearing that Valentine will get to her. Alec has to raise his siblings on his own after the Circle finds his parents. Angst and awkwardness. Clizzy and Malec AU.
1. Chapter 1

**This started out as a silly "lol what if Magnus raised Clary and Alec raised Izzy" AU with my friend but then I turned it into angst. Why am I like this? Why does this happen?**

 **In S1e10 of Shadowhunters, Meliorn mentions that in the other dimension, the war with demons was won and demons can no longer enter that dimension on their own. I wondered what that would do to the Clave in the earlier years after the war -and then I paired it up with the Circle. I love that pretty much all AUs can be canon via the show now, it's amazing.**

 **I'm also going to mention Infernal Devices characters, if you haven't read the books. They probably won't show up. Probably.**

 **Title from "Storm" by Ruelle.**

 **Disclaimer: I don't own the characters.**

Intro

Jocelyn brought Clary to Magnus' loft in Brooklyn when she was eight years old. She set down Clary's pink suitcase and her purple-and-blue backpack filled with Clary's toys. Jocelyn turned to Magnus as Clary squealed with glee at the sight of his cat. She rushed over to him and outstretched her arm so the cat could sniff her hand. She began to pet the cat, murmuring to him.

The two adults spoke to one another in hushed tones and Clary didn't catch much. She heard something about a Cup but she doubted they were talking about soccer.

Clary walked up to her mother, holding Magnus' big fluffy cat, whose nametag read _The Great Catsby._

"Please take care of her," Jocelyn told Magnus just as Clary stopped in front of them.

"Why can't I come with you?" Clary begged her mother.

The cat was heavy and he squirmed in her arms. Clary yelped when Catsby scratched her as he tried to free himself, and she dropped him onto the floor. He hurried away, tail puffed and swishing back and forth.

Her mother bent down to check Clary's scratch, though it wasn't bad. Clary just needed a Band-Aid. Jocelyn gave her a smile and stroked her red curls. "You're safer when you aren't with me, baby. I'm so sorry. Magnus will take care of you."

"When will you come back?" Clary asked.

Jocelyn hesitated. She pressed a kiss to Clary's forehead and didn't make any promises.

.

Magnus wondered when he'd gotten so entangled with the lives of Shadowhunters. He certainly hadn't _wanted_ to. Especially not when it came to Valentine's ex-wife and child.

He groaned and leaned back on his chair. Catsby sat in his lap and Magnus absentmindedly scratched the cat's head. He studied Clary Fray, asleep on the living room couch, a SpongeBob SquarePants Band-Aid now covering the scratch on her arm. Jocelyn had given him the same instructions she would to a babysitter: _She's not allergic to anything._ _No TV after eight pm; nine is her bedtime—nine-thirty at the latest, Magnus!_

(Magnus had let Clary stay up until eleven watching television.)

Well, Magnus thought begrudgingly, it wasn't quite like that. She had called ahead, in a hurry, said Valentine was onto her, that she would have asked Tessa and Will to take Clary, but they were in London and she didn't want them to risk coming to New York when Valentine was so close.

Part of him had wanted to argue that he wasn't exactly the safest option. He didn't keep as low a profile as Tessa and Will did.

"Tessa and Will have more connections with Shadowhunters," Jocelyn said.

Magnus understood her reasoning, but at least Tessa and Will would have much more experience in taking care of child, unlike him. And for how long would he have to take care of Clary? Jocelyn herself didn't know when she would be back. If she was going to be back. Magnus stopped that train of thought right there. Jocelyn loved her daughter. She would come back for her.

But, oh, God. He was going to have to call Tessa for help, wasn't he?

Only if he was truly struggling, he decided. They were probably already aware of the Valentine situation, but he would catch them up tomorrow. It was five in the morning in London, and although Will would no doubt still be awake, he wanted to tell them together.

Magnus sighed and snapped his fingers to magic a blanket on top of the sleeping child. Clary shifted, but didn't wake.

She had spent the hour after being dropped off as a crying mess. She vaguely recalled Magnus but it wasn't enough to put instant trust in him. She wanted to be with her mother. She felt _safer_ with her mother. Magnus didn't blame her.

Jocelyn had lingered for a few moments before departing. She had looked at her daughter, now watching television in the far side of the room, and then turned her gaze back to Magnus and swallowed.

"I don't want you to tell her," she'd told him. Magnus was about to protest that he was a _warlock_ and that it was ridiculous to expect him to keep the Shadow World a secret from Clary for too long, especially when it was the reason she was going to be living with Magnus in the first place. Before he could do so, Jocelyn continued, "But I won't stop you. When you think it's necessary, do it. It could be tomorrow, it could be in a month. But I know you have to tell her."

After that, she had left.

He had ordered Chinese takeout for dinner. Clary warmed up to him a little after that, but he still felt like a babysitter who would get in trouble for letting her eat unhealthily and stay up so late watching television. Only he was a babysitter who now had the responsibility of easing her into a world that her mother had wanted to hide her from. No pressure.

Magnus put Catsby on the floor. Despite Catsby's earlier disagreement with Clary, he gave Magnus a betrayed look and jumped up onto the couch, where he cuddled up with her.

"Traitor," Magnus muttered. He turned and went into his bedroom.

.

"Izzy, shut Max up," Alec said in a low voice.

He didn't look behind him, but he heard Isabelle shift and cover Max's mouth. His brother's quiet sobbing stopped and Isabelle sniffed. He hoped both of them would stay quiet. He knew it would be difficult –even now, he felt a lump in his throat. He couldn't allow himself to cry. They had to escape first. He couldn't risk being found by the Circle like his parents had been.

For the five years since they'd fled from the Clave to live among the mundanes, he'd been aware that this would be a real possibility. That Valentine Morgenstern would find his parents in search of the Mortal Cup. They had just hoped that it wouldn't happen. They had changed their last names. None of their children had runes. They had tried their very best to fit in the mundane world.

Alec had come home from school to a ransacked apartment. He had immediately known in his gut that Valentine found his parents. He looked at a photo of him and his family on the wall, now hung crookedly. There was a smear of blood on the white wall next to it. His stomach had felt like lead. The Circle members would have noticed the picture. He closed his eyes and sighed, thankful he'd been wearing his hood up so that it had been hiding his face when he entered his apartment building. Maybe there was a slim chance that the Circle members who were undoubtedly waiting for him and his siblings to return hadn't recognized him.

He'd almost stepped on his mother's stele. He took it and slipped it into his jacket pocket. His father's too, once he'd found that one, also on the floor nearby. No seraph blades in sight. Most likely the Circle members had confiscated them. Couldn't let the fifteen-year-old and his thirteen-year-old sister find them, could they? They might know how to use them. Alec had ground his teeth with frustration. They had fled the Clave when Alec was ten years old. He had never properly learned. He could barely even remember any runes.

He rushed to the room he shared with Max, dumped his books and folders on the floor, and stuffed as many of his and Max's clothes into his backpack as he could fit.

He'd gone to his closet, found a duffle bag, stuffed it with some of Izzy's clothes, menstrual pads, and some cans of food. He found a stash of his parent's money and put it in his wallet. It wouldn't last for long, but they needed anything they could get. He'd taken one last look around the apartment that he had called home for the past five years, and fled to Isabelle's middle school.

The three Lightwood siblings were together now, waiting in a subway station. A man was playing his violin in the corner. The instrument's case was open next to him, a silent request for money.

"Where are we going to go?" Isabelle asked. Alec turned this time to see that she and Max had eyes swollen from crying.

Izzy sniffed again and tossed a few coins from her pocket into the man's violin case. Alec had to bite back a reprimand when the man grinned at Isabelle and added a bit of a flourish to his playing for her. They needed all the money they could get, but it _was_ only a couple of coins. Isabelle cracked a smile at the enthusiastic violinist and Alec knew he couldn't take away this tiny bright moment from her with his worry.

Isabelle looked at Alec expectantly, and he remembered her question. Alec was tempted to go to the New York Institute for a brief moment. Their parents' steles were still in the pocket of his hoodie, and his fingers curled around them. But who knew what had happened to the Clave in all that time since his family had gone to hide from Valentine? Maybe it didn't exist anymore, or had been taken over by the Circle. He didn't know what had become of the other Shadowhunters and he didn't want to find out. He couldn't trust the Clave to protect them from Valentine. Not even living in the mundane world had done it.

"We're going to go in hiding," he finally replied as a subway train screeched to a halt. He started walking forward to get on the train. He didn't know if there were Circle members still following them, but he was going to try to lose them underground if possible.

"I thought we were already doing that?" Izzy asked, following him with her hand tightly gripping Max's.

"We'll have to do a better job of it than our parents," Alec said. He sat down and Max climbed into his lap, even though they were the only ones in this train carriage.

"I miss Mom and Dad," said Max. "Aren't we gonna find them?"

"We can't, Max," Alec said. "I told you. We don't know where they are. And it's dangerous to try to look for them."

"Then why can't we go home? I want to go home," Max said, and the tears were starting up again and Alec let his baby brother cry this time. He hugged Max tight to his chest and let him sob into his hoodie.

"Valentine is probably looking for us too, Max. We can't go back home."

"I don't even know what the Cup is!" Max said. His voice came out muffled. He leaned back to meet Alec's gaze and wiped his eyes. "I don't know anything. Why would they be looking for us?"

"We might know something," Isabelle said. "Alec and I are a lot older than you, Max. We know more stuff about Shadowhunters."

"Draw one rune," Max challenged, and when Izzy hesitated, he narrowed his eyes. "You can't remember!"

"I can remember one," she said and turned to Alec. She knew that he had the steles. She stretched out her hand as if to ask him for one of them.

"Our parents didn't want us to be Marked unless it was completely necessary," Alec said.

"I'd say being hunted down by Valentine makes it necessary," Isabelle told him. "I'm just going to draw the angelic power rune. It's the only one I can remember to do because it's so easy."

Alec shifted Max in his lap so he could reach into his pocket. He took out his mother's stele and looked at it for a moment. He handed it to Isabelle. "Put it somewhere discreet."

Isabelle pulled the collar of her shirt to the side to draw the rune on her shoulder. It wasn't as discreet as Alec would have liked, but he supposed it was better than other places she could have drawn it. Isabelle hissed as the stele burned her skin. Clearly she hadn't expected it to hurt.

She gave the stele back to Alec and looked at Max with raised eyebrows. Max looked at the rune black on her shoulder. "It looks like a tattoo."

"I'll be the only girl in my class with one," Isabelle said, leaning back on her seat. Alec didn't bother commenting that they probably wouldn't be going to their old schools after this. Izzy knew. She was a smart girl.

"Did it hurt?" Max asked. "It looked like it hurt."

"It burns a little," Izzy told him. "I'm okay, though."

They rode in silence until the next stop, where they got off. Max was nodding off, so Alec gave Izzy one of his bags so that he could carry their little brother as he slept. He didn't know where they were going to go.

But he was going to take care of his siblings. They were going to stick together. They'd survive.

 **Review?**

 _ **~Coqui's Song**_


	2. Chapter 2

**Thanks for the lovely reviews, everyone! Here's the next chapter.**

 **To note: this takes place around five years after the previous chapter leaves off. Because time-skipping is fun.**

Chapter One

Isabelle frowned down at her chemistry homework. She was beginning to question whether going to college had been the right decision. The third week in and she already felt stressed out of her mind. She'd been reluctant to go because she wouldn't be able to work full-time to help Alec out with rent, but Alec had insisted.

She'd gone to this coffee shop so that she could concentrate on her studying in a place outside of the apartment. It had opened recently and was adorned with rainbows, historic photos of LGBT movements, and a lot of positive quotes. This was the first time Izzy had come to this coffee shop and she was already in love with it.

She took a sip of her cooling coffee to focus on anything but her chemistry textbook. She emptied her cup and set it back down on the table. Isabelle rested her head on the book with a groan.

Izzy didn't realize that she'd fallen asleep until a barista woke her by shaking her shoulder. She sat up instantly, spitting out the few strands of her black hair that had ended up in her mouth. She looked around the shop; a band was setting up to play live music, two girls were holding hands and talking to each other in low voices, and a few other people her age were staring at their laptops.

"I'm sorry," said the barista, bringing Izzy's attention back to him.

"No, no," Isabelle said, stifling a yawn. "How long was I asleep?"

He shrugged. "Half an hour?"

"Right." She'd forgotten if her coffee cup was empty, so she picked it up and shook it lightly. There wasn't anything in it so she got up to throw away her trash. Izzy turned back to her table and stared at her pages of notes. She sighed inwardly.

Isabelle decided that studying was a lost cause. She put her homework into her backpack and ordered another coffee as she watched the band (which really was only made up of two people) set up and test the microphone.

Instead of going back to her table, she made her way to one of the couches near the stage. She leaned back and made herself comfortable.

The band introduced themselves as Champagne Enema. They were pretty decent, though they started off with a couple of covers. Izzy wondered if they had any original songs. In the middle of their second song, a girl sat down next to her and fiddled with her bag to take out her wallet, muttering about how she was late. Isabelle scooted an inch to the side to give her more space. The girl brushed her red curls out of her face and turned to Isabelle.

"Can you watch my bag while I get a coffee?" she asked.

"Of course," Isabelle replied.

The girl thanked her and made eye contact with the band's front man. She waved her wallet, mouthing "Sorry." She made her way to the line and Izzy didn't look away from her until she disappeared behind the taller people in the front of the line.

It took two more songs until the girl came back with a coffee cup in hand. She thanked Isabelle for watching her bag again and turned to the band and smiled. She had a way of smiling that made her nose scrunch up.

"You know the band?" Izzy asked.

The girl started. She hadn't expected conversation, but when she answered she was more than friendly. "Oh, yeah, the lead singer Simon is my best friend. This is his first gig here, and I promised I'd come. I was a little late but hopefully he won't kill me for it."

Isabelle laughed. "Hopefully. Do they have anything original?"

"A couple of songs," she said. She smiled again, at Izzy this time, the same nose-scrunching smile as before. It was impossibly sweet. "My name's Clary."

"I'm Isabelle." She grinned in return. "So, do they have a demo?"

Clary tipped her head to the side. "I think I can get one for you."

They let the conversation drop between them until the band's break. Clary stood up and hugged Simon and the other member of the band, a pretty girl named Maureen. Clary came back to Isabelle and told her that they'd bring demos next week if she really wanted one.

"Is that a tattoo?" Clary asked, pointing to Izzy's shoulder. Izzy bit the inside of her cheek. She'd been less careful since last year, but she'd wanted to wear this tank top today. It showed off her angelic rune but she'd assumed that everyone wouldn't ask about it.

She was a little guarded about Clary now, but she played it off and nodded. "Got it a little while ago."

Clary looked like she wanted to ask more, but she grinned. "It's cool."

Isabelle quietly thanked whatever higher power could be out there. Even five years after Valentine had killed her parents, she was looking over her shoulder for Circle members. Her fighting skill was limited and she didn't remember many runes, nor did she have a seraph blade. She and her brothers were easy targets. Their only choice was to hide, and Izzy had made an impulsive decision at thirteen to Mark herself with an unmistakable rune, one every Shadowhunter had.

Even if the person was a mundane, any attention given to her 'tattoo' made her heart jump to her throat every time.

Hopefully Clary was just a mundane, like everyone else who had asked about it. Hopefully Clary wasn't a Circle member.

Clary unlocked the door to the loft and let herself in, cautious. She didn't want their new kitten running outside of the loft. Chairman Meow had gotten out two weeks ago and she and Magnus had gone out of their minds with worry for a good six hours. She closed the door behind her and threw her keys on the kitchen table.

Chairman Meow jumped down from where he sat on Magnus' lap and hurried over to rub himself around Clary's ankles. Magnus leaned back on the couch and turned to look at her. The television was on, but that was currently the only thing giving off light in the room.

It wasn't any surprise that Magnus was still awake. It wasn't really that late. It was around eleven right now. After the gig, Clary, Simon, and Maureen walked around the city for an hour or so. She'd invited Isabelle, but she'd needed to go home.

"You're here early. Was the party lame?" Magnus asked.

"Wasn't a party. Simon had his first gig at that new gay coffee shop, remember?"

Magnus arched his eyebrows. "I don't know if I like your tone. Is something bothering you?"

"Sorry. I'm just confused about something that happened tonight," she said.

Magnus moved over on the couch and patted the space next to him. She dropped her bag and collapsed on the seat. The Chairman leaped up to the couch and butted his head against her chin and she exhaled hard through her nose so she wouldn't sneeze.

"I met this girl tonight," she started.

"Did you get her number?" Magnus asked, leaning forward.

Clary rolled her eyes. Sometimes Magnus liked to butt into her love life a little too much. He tried too hard to be the embarrassing father. "Yes, but that's not what this is about. She had an angelic rune on her shoulder."

"A Shadowhunter," Magnus said. "You saw another Shadowhunter?"

"She only has the one rune though," said Clary. "Nothing else."

Magnus shook his head. "I wouldn't worry too much about it, biscuit. No Circle rune, right? Just the angelic power rune. She's not a member of the Circle. Whatever her story is, I doubt she's associated with them. I think you should glamour your runes around her, though."

Clary nodded and turned her head to whatever the television was showing. She began training as a Shadowhunter when she'd turned twelve years old, with the help of some of Magnus' friends. Clary had realized that she had a talent with runes unlike any other Shadowhunter. The runes she drew were more powerful and lasted longer. She had even learned to create new runes, ones that Magnus and his friends had never seen before. They weren't in the Gray Book.

They didn't know why she had this ability, but it gave Magnus more cause to keep her hidden. If Valentine Morgenstern found out about her, there was no telling what he would do with that sort of power. Clary would die before she would let her father use her abilities, but she didn't necessarily want it to come to that.

Of her created runes, the most important one was a special glamour that hid her runes so that she appeared to be a normal mundane. She used it nearly every day. Clary didn't want the Circle to find her. Despite not having heard of the Circle in several years, she was always prepared. She even tried to stay out of the Clave's way. It was hard with Magnus as the High Warlock of Brooklyn, but they'd managed to keep her existence a secret from the Clave even as she trained.

Coming across another Shadowhunter was unfamiliar territory. It had been bound to happen, but it sent alarms ringing in her head.

She picked herself up from the couch and went to her room to change. She threw her phone on the bed. Just as she had put on her pajama pants, her cellphone buzzed.

 _ **Izzy**_

 _I'll definitely take one of those demos._

 **Reviews are appreciated!**


	3. Chapter 3

**This was a fun chapter to write.**

 **A note: I added a few paragraphs to last chapter because I realized there was a bit of a plot hole concerning runes and glamouring them, and it bothered me enough to actually fix it.**

 **Again, a thank you to the lovely reviewers!**

Chapter Two

Alec wondered at what point he should stop waiting up for Izzy. She said she would be going out tonight –not to study, but with a friend. The thought shouldn't have worried him. He kept trying to tell himself that he was being overly cautious. It was good that Isabelle was making friends and enjoying herself. She should, and after all their struggles, they deserved it.

It was just late. Alec checked his cellphone to look at the time. It read 2:37 am. Alec had sent Max to bed more than three hours ago, and texted Izzy. There hadn't been a response. Izzy lived her life less carefully than Alec did. She always said that it was necessary to be wary and look out for Circle members, but not at every moment of the day.

No matter how Alec's instance might annoy her, she always called or texted back.

Alec was also worried because last week Isabelle had come home and mentioned that a girl had asked about her rune. He had hounded her for any and all details.

"She said her name was Clary. I met her at the coffee shop I told you about—" Izzy cut herself off and grinned. Her eyes had the teasing glint they always did when she was about to start poking at him about his love life.

"Drop it. I'm not getting a boyfriend. We've been over this," Alec said. "Tell me about this Clary."

"Well, she's a couple of inches taller than me, she has fiery red hair, it's kind of curly too. _Muy bonita_. Green eyes, long legs. Her smile is the cutest I've ever seen, and she has _great_ boobs," Izzy said. She paused and met his gaze, unrepentant. At seeing Alec's horrified expression, she laughed.

 _"Izzy."_

"All right! Fine. Her name is Clary Fray. She noticed the rune and called it a 'tattoo,' then she said it looked cool. She didn't have any runes on her. I was at a gay coffee shop, Alec. She was probably hitting on me." Isabelle inspected her nails. She seemed to be trying too hard to be casual.

"Okay, now tell me what you really think," said Alec.

"I _think_ I'm going to hang out with her sometime, and try to see if I can find out anything else," she said. "But odds are, she's just a curious mundane."

"You don't sound too convinced."

Isabelle hesitated. "She looked at it as if she knew what it meant. But she didn't say anything."

Alec tapped his index finger on his knee and leaned back. "Whatever you decide to do, just… be careful."

Isabelle had stood up and walked over to him. She leaned into him and wrapped her arms around him. He returned the hug and felt her bury her face into his shoulder. She turned her head and pressed a kiss to his cheek before she pulled away. "I will."

If Isabelle was out with this Clary Fray –and Alec suspected that she was—this was certainly _not_ careful. Alec had texted his sister four times without a response. He didn't know what more he could do except wait for her to get home.

Well. There was one thing he could do.

His eyes drifted to his dresser. It was where he kept his parents' steles.

There were days he wanted to get rid of them. So that he and his siblings could live completely as mundanes. But he kept them because part of him insisted that he would need the steles one day, and that getting rid of the only things that linked him to his parents and his heritage would be like losing himself.

There were other days still that he wanted to Mark himself all over his arms so that his identity as a Shadowhunter would be unmistakable. A silent challenge to any Circle members that might be onto them.

Today was one of the latter days. His fingers itched for a stele. He remembered how it felt to be Marked; Isabelle had drawn the angelic power rune on him a few years ago. It had taken him a while to agree to it, but Izzy just didn't let it go. Finally he had pushed up his sleeve and let her draw the rune. It had burned at first. But with it came a burst of power.

"How do you feel?" Max had asked.

"Like a Shadowhunter," he'd replied.

Alec walked to his dresser and opened a drawer, digging around for the steles. His hand felt cold metal. He closed his fingers around one of them and brought it out. This one was his father's. Bronze and carved with different runes. He studied them as though one of the runes would be the one he needed. He wished that he could just tell the stele what he needed, and that it would press against his skin and move of its own accord in the shape of a tracking rune.

He closed his eyes and tried to remember. Ten years ago, before they'd left the Clave, he had used flash cards to memorize the runes. They had left the flash cards in the New York Institute, thinking there would be no use for them.

He just needed to remember the tracking rune. The hand that held the stele was trembling. He couldn't mess this up. He went over all the ones he could recall in his head. _Angelic power_. Easy. _Nourishment_. The _iratze. Clairvoyance. Deflect_.

 _Tracking._

He hoped to the Angel that it was the right one.

He went to Isabelle's room and took one of her favorite necklaces. She'd worn it yesterday. Hopefully her presence would be strong enough to lead him to her. Without a _parabatai_ , the rune would be weak but Alec had to try. He still hadn't drawn it. There would be no coming back from this.

He gripped the stele tightly and drew it over his other wrist. It burned and Alec gasped. It hurt more than the angelic rune had, but he closed his eyes and concentrated on the necklace and on finding his sister. The rune was leaving him only with the faintest impression of where Izzy was.

Alec opened his eyes and left her room to wake Max up.

His younger brother blinked up at him with bleary hazel eyes. _"¿Qué?_ "

"It's past three in the morning and Izzy still isn't home," Alec said. "I'm going to get her. Do you want to come or can you stay by yourself for a few hours?"

"'m fine, I'll just be here sleeping," he said, closing his eyes again and turning away.

"I'll text you if anything happens. You know what to do, right?"

"Run, meet you at the nearest subway station. Worst case scenario, I go to the New York Institute," Max said. He sounded half asleep, but they'd gone through this plan so many times that his kid brother could recite this in his sleep.

Alec stroked Max's hair and leaned over to kiss his forehead. "Good. I'll see you soon."

Magnus usually let Clary have free reign. She was a good girl and knew not to get into too much trouble. He had to admit, however, that he was currently worried out of his mind. Clary had never been out this late before, and he couldn't help the nagging fear that Valentine had found her.

She had learned to glamour her runes. Runes tended to fade on Shadowhunters after a long time of not using them, but Clary used them. Clary wanted to use them even without demons running around the streets. She wanted to be prepared if she ever saw a Circle member. After twelve years, she still wanted to find her mother.

But she also needed to be hidden. So she created a rune that would make them vanish on her skin. Magnus knew they could still be activated and could still pulse with energy and power, but they couldn't be seen. It was handy and essential for her, and was a large reason that—as far as Magnus knew—neither the Clave nor the Circle was aware of her.

Just as Magnus was about to rush to Clary's room to get her sketchbook or something equally as important to her so that he could track her, the buzzer rang.

Clary never used the buzzer. She had a key.

It was four in the morning. Magnus hadn't set up any appointments today at this hour. He walked over and pressed the button. "Who is this?"

"My name is Alec. Does Clary Fray live here? I found her at a club and she said she lived here."

"Yes, but I'm afraid Clary Fray is very gay, so if you would be so kind as to help her up the stairs and then leave," Magnus said, and let him in.

A few minutes and there was a knock at his door. When he opened it, he found Clary holding on to a man's arm to steady herself. Her hair was damp with sweat. Her mascara clumped and the rest of her makeup smudged.

"Oh my God," Magnus breathed, and threw his arms around Clary.

She stumbled back a step and rested her head on his chest. "I'm okay, Mags."

Magnus pulled away from the hug to give her a glare. "Are you drunk?"

Clary held up her right hand with her thumb and pointer finger close together. "Little bit."

There was an entire lecture that he opened his mouth to begin, but he closed it and sighed. "Get a drink of water and go to bed. We'll talk about this later."

Clary nodded and brushed past him. He heard her giggle and coo at Chairman Meow. He looked at the man who had brought Clary home. He was taller than Magnus, with messy dark hair and honest hazel eyes. He looked a little embarrassed.

Magnus hoped that his face didn't look as enamored as he felt.

"I didn't mean to make it seem—I never hit on her, I didn't—I mean, I'm not—" Alec said, looking horrified. Magnus had seen that expression a thousand different times on a thousand different faces. He decided not to press.

"Thank you for bringing her home," he said, smiling. "Sorry to give you trouble. She's a good kid most of the time."

"Are you her…?" Alec trailed off, confused.

"Guardian, adoptive parent, babysitter. Take your pick," Magnus said. He stretched out his hand. "Magnus Bane."

He saw a flash of recognition in Alec's eyes. He seemed to hesitate before giving Magnus his hand. Alec's sleeve rode up and Magnus saw the strokes of an angelic rune on the inside of his arm. He tried not to stare at it as they shook hands.

When he met Alec's gaze again, he knew that his reaction had not been unnoticed. There was a fear in there, but also curiosity, and strangely enough, trust.

"Alec Lightwood."

The surname came out as though he was not used to saying it, but it was hard with an affirmation of who he truly was.

A Shadowhunter.

 **Reviews are greatly appreciated!**


	4. Chapter 4

**A short-ish chapter with only one POV this time. I think I'll start writing only one POV in a chapter from now on.**

 **Thanks for the reviews!**

Chapter Three

The sunlight filtered through the curtains in Clary's bedroom. She opened her eyes and groaned, twisting around so that she didn't face the window. She covered her head with the pillow and willed herself to go back to sleep so that the pounding headache could go away. Just as Clary was on the edge of falling back into sleep, she felt a sudden weight land on her chest.

Her eyes flew open. She looked out from under her pillow. Chairman Meow had jumped onto her bed and decided to settle on her. "No."

It came out less as an order and more as a whine.

"Good morning, sunshine," came Magnus' voice from her bedroom door. So that was how Chairman had gotten in her room.

Clary sat up and yawned before fixing Magnus with a glare that she hoped was deathly. More than likely she only looked like a disgruntled cat. This time when she spoke, she was firm and short. "No."

"Come on, Clary," said Magnus. He was holding a glass of water in one hand and a couple of small pills in the other. "I brought some ibuprofen."

"'S too early to wake up," Clary said, but she mustered enough energy to drag herself from bed and over to Magnus. She took the pills without a word and downed the entire glass of water.

Magnus waved his hand and the empty glass vanished from her hand. When she was younger, this kind of thing had made her flinch back. Magnus used his magic for even small things like putting away a cup. Now she was used to it. Clary stared at her hand, still curled in a semicircle as though it was holding the glass, and frowned. She had wanted to get more water.

"It's nearly noon," Magnus told her. "Maybe if you weren't out partying until four in the morning, this wouldn't feel like such an early start for you."

Clary scrunched her nose. Part of her wanted to mention that he owned a club and had spent many late nights out, but Magnus was making an attempt at being parental. It wasn't often that he was like this. It wasn't the partying that had him upset.

"No calls. No texts," he said. "Nothing until that boy Alec brought you home."

Her head felt like it was a drum. The ibuprofen wouldn't start to take affect for a few more minutes. She was glad that he kept his voice low. "I'm sorry."

"No excuses?" Magnus asked. "No 'my phone battery died,' no 'I was too drunk,' nothing?"

She hesitated. Clary bit the inside of her cheek and brushed past Magnus, signaling him to follow her until they reached what could be called their living room. She collapsed on one of the couches and waited for Magnus to sit on the other side before she spoke. "This isn't an excuse. I don't have an excuse for not calling you. I should have called you and I didn't."

"And?" Magnus prompted. He knew her well enough to know that there was more to her story than just not calling him.

"I saw Circle members last night," Clary said. Before Magnus could scold her for that, she added, "I didn't do anything. I didn't approach them. I didn't follow them. My runes were glamoured; I looked like a normal mundane. I was with Izzy the whole time."

"What happened with her?" he asked.

"She recognized them," Clary said. "She saw the Circle runes on their necks and got all pale."

She thought back to last night. Parts of it were blurry, courtesy of the alcohol, but she remembered the more important bits. After Simon's gig at the coffee shop where they had met, she and Isabelle had gone to a club.

They flashed their fake IDs and started drinking. The drinks loosened Clary up enough that she started flirting. Isabelle smiled and took a strand of Clary's hair, twirling it around in her fingers. She said that her hair felt so soft. Clary remembered how heated her cheeks had felt and the flutter in her stomach even now. She replied with something about using some special shampoo.

Isabelle's flirtatious little smile dropped suddenly. She looked past Clary at something far behind her. Clary turned around to follow Izzy's gaze to see a man dressed all in black, wearing shades indoors. At night. Clary almost rolled her eyes before she noticed the Mark on his neck.

The Circle rune was black against his pale skin and noticeable from fifty feet away. Clary had to double-check to see if her runes were glamoured, and let out a breath when she saw they were.

Still, her fingers itched for her stele and her seraph blade. She'd hidden them in her jacket.

Isabelle however was tense. She shot a look at her shoulder; she had worn a jacket as well, covering the angelic power rune.

"We need to go," Clary said. "Now."

She paid for the drinks and tipped the bartender, grabbed Isabelle by her upper arm, and walked briskly to the exit. Izzy was lucky not to trip over herself in her heels. She giggled with her nerves. After they left the club came the questions.

"You know about Shadowhunters?" Izzy asked.

"I am a Shadowhunter."

"Me too. Kind of." Kind of. Clary made a note to ask her what she meant about that later. Hopefully she remembered to. "You're not a Circle member?"

"No."

"So then you're a member of the Clave?"

"Wrong."

Izzy furrowed her brow. "How can you be a Shadowhunter without being part of the Clave?"

Clary laughed. She laughed more than the question warranted. They stumbled into another club, blocks away from the one they were at previously. She never answered.

"What happened to the Clave?" Isabelle asked.

"I don't want to talk about the Clave," Clary said.

She ordered them drinks because they needed to take their minds off of the Circle members. And take their minds off of the Circle members they did.

Clary told all of this to Magnus. She remembered a lot of dancing, a lot of flirting after that. Songs with beats that matched the pounding of her heart. Izzy's hand brushing the hair off her shoulder.

She didn't remember when Alec had come looking for his sister. The details were blurred in her mind. But she knew that Alec had taken her home.

Magnus was quiet for a long time. He didn't look angry. Clary waited in agony for him to speak. She didn't know what she expected from him.

"You saw a Circle member," said Magnus, in a voice that withheld any emotion, "and didn't call me."

"Nothing happened," Clary tried. "I left and I took Izzy away with me."

Her mind flew through other things she could say. All she could think about were the things they could do now with this information. They couldfinally start the search for her mother. Clary had trained for years for a chance like this. She knew how to fight. She was as good a Shadowhunter as any trained by the Clave. All she needed to do was track them down.

Unfortunately, Magnus wasn't feeling sympathetic today. She knew he would have forgiven her partying all night without a phone call. He couldn't let something like this go quite as easily.

"Clary Fray, you're grounded."

 **Reviews are greatly appreciated.**


	5. Chapter 5

**Sorry I took so long in updating! I got a bit of writer's block, but I'm back now!**

 **Thank you for all of your lovely reviews!**

Chapter Four

Isabelle sat beside Max and watched him as he played Pokémon. It was strange, she thought, how if their parents hadn't run from the Clave, they wouldn't have let him bother with many mundane things like this. Max would have been studying Shadowhunter history and preparing to receive his first runes.

If the Clave still existed, that was.

Izzy couldn't get Clary out of her mind. She'd admitted to being a Shadowhunter, but was neither a Circle member or part of the Clave. Clary lived in a state of limbo akin to the situation of Isabelle and her brothers. Hiding. Observing.

The difference was that Clary knew things that Izzy and Alec didn't. Isabelle, Alec, and Max hid as mundanes and couldn't quite break out of it. Clary could hide as a mundane but she also had an access to the Shadow World that Isabelle and Alec didn't.

She lived with Magnus Bane, the High Warlock of Brooklyn. She'd been _trained_ ; that much was obvious. Clary had taken one look at the Circle member Friday night and her hand had gone straight to the inside pocket of her jacket. When Isabelle had looked closely, she noticed a stele. Clary hadn't used it, opting to appear as a normal mundane.

Isabelle stared and stared. Clary had a stele but no runes. It didn't make sense to her, but it was clear to Izzy that Clary chose to use her Shadowhunter powers or her appearance as a mundane to her advantage.

Izzy didn't have that option. She'd never been trained and neither had Alec. The closest she came to knowing anything about combat was through a self-defense class for girls that she'd gone to in high school.

She wanted to know the things that Clary knew.

Max closed his DS, and it snapped Isabelle out of her thoughts. He stood and made his way to the kitchen, yelling out, "Do we have any leftover pizza?"

"You're the one in the kitchen," Izzy said, standing up to follow him. If there wasn't any pizza, she'd have to take him out for lunch. Alec was at work and there was no way in hell that Max would eat anything she cooked.

Seeing that there were no leftovers in the fridge, Isabelle went to her room to put on shoes and grab her purse. Izzy grabbed Max's hand and they left the apartment.

"What do you want to eat?" she asked.

Max's eyes lit up. "Pizza!"

"Max, we had pizza yesterday and the day before. Try again," Izzy said, smiling down at her little brother. "And nothing fancy. Alec and I have to pay the rent this week."

"That's funny. You weren't thinking about having to pay the rent when you went out on Friday," Max said.

Izzy raised her eyebrows. He shut his mouth and looked away. Max sighed in the way a grown man would when told he wouldn't be able to get a last minute plane ticket. He stared at the McDonalds across the street with distaste before settling for it.

"We're only here because I'm too hungry to take time in deciding what I really want," Max said as they entered. "Just get me some chicken nuggets I guess."

"Do you want a Happy Meal?"

"Of course I want a Happy Meal. I'm not twenty," Max said.

"I don't know, I think a lot of twenty-year-olds like Happy Meals. Some of those toys are really cool," Izzy replied with a laugh.

The line was long but it went by faster than Izzy expected. She and Max sat down with their meals.

Her phone buzzed in her pocket. She brought it out saw that it was a text from Clary. Izzy's heart started to pound. She opened the message.

 _ **Clary**_

 _Hey Iz. We kinda need to talk about what happened on Friday_

Isabelle looked up from her phone to look at Max. He was too busy eating to pay attention to what she was doing.

She typed, _The flirting or the Shadowhunting?_ but didn't send it. It wasn't that she was afraid of being too forward. That had never been a problem for her. But after seeing that Circle member, she knew she had bigger things to worry about.

Instead, Izzy responded with, _Are you going to tell me what you know?_

 _ **Clary**_

 _Only if you tell me what you know_

 _It isn't much,_ Isabelle sent.

 _ **Clary**_

 _That's okay. When are you free?_

Izzy was technically free at the moment, but she wanted Alec to hear whatever Clary had to say. He'd been angry with Izzy yesterday. They'd been in real danger. He still didn't trust Clary, but after seeing that she lived with a warlock, his suspicions about her being in the Circle had dropped.

Besides, if she went now, she would have to take Max. And she didn't want to discuss the Circle with her eleven-year-old brother in the room. It wasn't that she thought he couldn't take it, or that she wanted to hide things from Max. She wanted to protect him from the Shadow World and this felt too much like pushing him off the deep end.

It would have to be during the week.

Izzy told Clary this and suggested places they could meet up, but Clary texted her back saying that Magnus had grounded her. Isabelle tried to keep a straight face but failed.

"What are you laughing at?" Max asked.

"Just something my friend said."

Izzy sent Clary a final text saying that she and Alec would be at the loft on Tuesday and put her phone away.

"Are you hiding something from me?" asked Max.

"We don't hide things from each other," Izzy replied. "You already know about what happened Friday night. Clary just wanted to follow up with me."

"What do you think she knows?"

"Hopefully a lot."

Max dipped one of his fries in the ketchup. He threw the fry in his mouth and chewed it thoughtfully. "Alec doesn't know if he trusts her."

"I know," Isabelle said. She took a sip of her soda. "I trust her. And we'll tell you everything after we meet with her. "

"You're not bringing me?" Max said.

"You'll be in school."

Max widened his eyes. "But what if school isn't safe for me? What if one of my teachers is a Circle member?"

"You're going to school." Isabelle stole one of Max's fries, and that was that.

.

Despite the fact that Izzy had told her in advance that they were coming over, Clary looked surprised when she opened the door. She let Alec and Isabelle in, telling them to hurry so the cat wouldn't escape. It was a little tabby named Chairman Meow, and Izzy cooed at him and stretched out her hand for him to sniff. He rubbed his face on her hand and Izzy giggled.

"We aren't here to play with the cat," Alec said.

Chairman Meow took notice of him next and pressed himself against Alec's leg. He looked down at the cat, puzzled.

"He likes you guys," Clary said, smiling down at Chairman Meow for a moment before looking back up at them. "Can I get you anything? Coffee or tea?"

"This isn't a social visit—" Alec protested.

"I'd love a cup of coffee, actually," Izzy said.

Clary brightened and turned to Alec expectantly. He sighed and waved in the sort of universal gesture for ' _sure whatever_ ,' and Clary went to the kitchen. Alec and Isabelle sat on the couch while they waited for the coffee.

"Magnus isn't here," Clary called out. "He had some errand but I'm sure he'll be back soon. Do you take milk and sugar?"

Izzy and Alec both told Clary how they liked their coffee, and soon she came out with a tray and three coffee mugs.

"So you're a Shadowhunter?" Alec asked.

Clary had been taking a sip from her mug, but she set the mug down on the table. She nodded and brought out a stele from her boot. She traced a rune over her arm and black Marks appeared on her skin. "I keep forgetting to deglamour them at home."

"You can glamour runes?" Izzy asked.

How did her parents not know this? Shadowhunters were easily identifiable by their runes and if there was a way to hide them, why didn't her parents take it? Alec and Izzy had made sure to put the angelic rune in discreet places.

Clary had runes that snaked up and down both of her arms. There was a rune on Clary's neck and on the back of her right hand. And why couldn't Clary have them in visible places? She had a rune to glamour them when necessary.

"Yeah. It's pretty helpful when you need to hide from the Clave," Clary said. Chairman Meow jumped on Clary's lap and she scratched the cat's ears.

"So the Clave still exists?" Isabelle asked, leaning forward. It was something that she and Alec had been wondering for many years.

"Yes," Clary said. "They're a bunch of cowards but yes, the Clave still exists."

"But why do you need to hide from them?" Alec asked.

Izzy wanted to know the same. The Clave might still exist but who was to say that the Circle of Raziel hadn't taken it over?

Clary blinked. She was quiet for a moment, as though agonizing over what to reveal to them. She took another drink and tapped her fingernails on the mug. Finally, she took a deep breath. Izzy wondered if it was a trick of the light, or if those were tears in Clary's eyes.

"My father is Valentine Morgenstern."

 **As always, reviews are appreciated!**


	6. Chapter 6

**Erm. Sorry for the delay in updating.**

 **I want to thank the reviewers for being patient. Also, I want to be clear that I take aspects from both the show and the books. This fic is mostly based on the show because I prefer it to the books, but I take things from the books as well to create a unique universe.**

Chapter Five

Alec stood up. He had been hesitant to trust Clary, but after all of Isabelle's assurances that she wasn't in with the Circle, this was a blow. How was he supposed to believe anything Clary Fray—Clary _Morgenstern_ said? Her father had killed his parents, killed innocent Downworlders. All in search of the Mortal Cup.

"Alec," Izzy said, grabbing the hem of his sweater and tugging on it. Alec swiped his sister's hand away and inched out of her reach. He wasn't going to sit back down.

"Your father," he said to Clary, "is _Valentine Morgenstern_. And you expect me to trust you? He killed my parents!"

"He took my parents away from me too!" Clary snapped. Her jaw trembled and she blinked the tears from her eyes. She stood and glared at him. "Just listen to me. Please. I need your help."

"Alec, she doesn't have a Circle rune," Izzy said softly. "She lives with a Downworlder. Please. We need her help too. She's a Shadowhunter who isn't with the Clave and isn't a Circle member. She's like a saving grace for us."

"We don't know she isn't secretly with the Circle," Alec said. "Are you looking for the Mortal Cup, Clary Morgenstern?"

"Fray," Clary said. She clenched her fists. "It's Clary Fray—or Fairchild if you _must_. Don't call me Morgenstern. All Valentine has ever done to me is bring me pain, and I've never even met him. My mom dropped me off here when I was eight. I didn't know anything about the Shadow World then. All I knew was that Luke, the man who I'd thought of as my father, had been kidnapped, and my mother was leaving me. I don't know where they are. They might be dead. But the High Warlock of Brooklyn raised me since I was a child and you _dare_ insinuate that I'm in the league with Valentine."

"But are you looking for the Cup?" Alec asked again. The sad details of her backstory didn't interest him. He only needed to be sure if he could trust her.

"To stop Valentine from getting it, yes," Clary said. "I don't have any leads, but as far as I know Valentine doesn't either."

"You're sure he doesn't know where it is?" Isabelle asked.

"We'd know if he had it," Clary said. "New Shadowhunters would be popping up like dandelions."

She hadn't taken her stare off of Alec. She was daring him to push more, he could tell. He thought about how this girl had been taken in by Magnus. He vaguely remembered hearing about Magnus Bane's indifference towards Shadowhunters as a child. Alec had never met him before the night he had taken Clary home, but the affection with which Magnus talked about her had been clear enough.

Trust was going too far. But he would work with Clary.

The door opened and the three Shadowhunters turned to see Magnus unzipping his jacket. He tilted his head and took in the scene. He introduced himself to Izzy, who introduced herself back. His gaze rested on Alec for a second longer than Izzy. Alec twitched and didn't meet his eyes. Finally when he looked at Clary, he raised his eyebrows.

"I assume you've told them, then?" Magnus asked. He had noticed Clary and Alec's confrontational body language. Alec took a step away from Clary and relaxed his shoulders. Magnus waved his hand. "Please. As though I wasn't reluctant to take in Valentine's daughter. But she turned out pretty well."

" _Thank_ you," Clary said. "Now can we figure out what we're going to do about this now that we're all here?"

"About what?" Magnus asked.

"Finding the Mortal Cup," Alec said, just as Clary said, "Finding Mom and Luke."

They looked at each other again. Alec frowned. Clary's priorities were far different than his. He'd given up on finding his parents. He knew they were likely dead. Clary's parents had been gone for a decade. What made her think that they were still alive?

"I thought you wanted to find the Cup so that Valentine couldn't get to it," said Alec.

"And only my mom knows where it is," Clary said. "She took it from him and hid it. We tried to see if I could remember anything about its whereabouts—I went to a Silent Brother—"

"You went to see the _Silent Brothers_?" Izzy asked, eyes wide. "I thought you needed to hide from the Clave."

 _"A_ Silent Brother," Clary corrected, her face stony. She did not want the subject to be pushed further. "Magnus tried everything he could. We can't summon demons anymore now that the portals to other dimensions have closed. I don't know where it could be. So if we want to find the Mortal Cup, we have to find my parents first."

"What makes you think your mom hasn't been killed by Valentine?" Alec asked.

Clary and Magnus shared a look.

Magnus walked over to the couch. He sat down beside Isabelle. Blue sparks appeared at his fingertips and suddenly he was holding a cup of Starbucks coffee. Alec stared. Magnus took a sip and frowned. "Needs more sugar." He looked up at Alec. "Valentine wouldn't kill Jocelyn. If he still doesn't have the Mortal Cup, it's safe to assume that she is alive."

"What about Luke?" Clary asked.

Alec got the feeling that this was a question she asked frequently, a question she hoped would have a different answer. It made him wonder just what Clary had been doing all these years. She seemed to have training. She'd gone to the Silent Brothers. How was it that she didn't have any leads whatsoever?

Magnus simply shook his head. "That's impossible to tell. They were _parabatai_ once, but they betrayed each other."

Clary nodded. She sank down beside Magnus. "Are we going to have to go to the Clave? Do you think they know more than us?"

"Absolutely not," Magnus said. "We can do this on our own."

"We've been doing this on our own," said Clary. Her voice tightened. "It isn't working."

"That's why you have us, isn't it?" Isabelle put in. "We're not part of the Clave. By all accounts, the Clave probably thinks we're dead. But we're Nephilim. And we're here."

Clary pressed her lips together. She ran her gaze between Alec and Izzy, and back again. She nodded. Clary brushed cat fur off of her jeans and stood. "That's right."

She walked over to a wall and glanced at Magnus, crossing her arms. Magnus sighed and snapped his sparking fingers. A glamour over the wall went down, revealing a small collection of Shadowhunter weapons: a couple of steles and seraph blades, even a whip and bow and arrows. Not enough weapons for an army. Just enough for the three of them.

But more than what Alec would have expected.

"How did you get these?" Alec asked.

Magnus grinned. There was a glint in his eye. "I have connections."

Clary cleared her throat, and Alec and Izzy looked back at her. She took a seraph blade off of the wall and weighed it in her hand. She glanced up at them. "If we're really going to stop Valentine, you two need training."

She held out the seraph blade and waited.

Alec felt a thrill go down his spine. Drawing all the runes would do nothing if he couldn't hold his own in a fight. Being trained by little Clary Fray was less than ideal, but he would do it. Clary was all he and Izzy had, after all.

Alec stood and walked to her, holding out his hands. Clary placed the sword in his hands. At his touch, the runes etched on the blade glowed.

Time to begin.

 **Reviews are always appreciated!**


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